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         UniProtKB/Swiss-Prot protein knowledgebase release 2014_02 statistics





1.  INTRODUCTION



Release 2014_02 of 19-Feb-14 of UniProtKB/Swiss-Prot contains 542503 sequence entries,

comprising 192888369 amino acids abstracted from 226190 references. 



266 sequences have been added since release 2014_01, the sequence data of

108 existing entries has been updated and the annotations of

468099 entries have been revised.



Number of fragments: 9077

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 35870





Protein existence (PE):           entries     %



1: Evidence at protein level        81710   15.1%

2: Evidence at transcript level     62411   11.5%

3: Inferred from homology          380794   70.2%

4: Predicted                        15701    2.9%

5: Uncertain                         1887    0.3%



The growth of the database is summarized below.



   





2.  TAXONOMIC ORIGIN



   Total number of species represented in this release of UniProtKB/Swiss-Prot: 13056



   The first twenty species represent 114353 sequences:  21.1 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5445

                            2x: 1898

                            3x:  995

                            4x:  646

                            5x:  467

                            6x:  394

                            7x:  288

                            8x:  223

                            9x:  212

                           10x:  122

                       11- 20x:  694

                       21- 50x:  417

                       51-100x:  213

                         >100x: 1042





   2.2  Table of the most represented species



  ------  ---------  --------------------------------------------

  Number  Frequency  Species

  ------  ---------  --------------------------------------------

       1      20270  Homo sapiens (Human)

       2      16658  Mus musculus (Mouse)

       3      12665  Arabidopsis thaliana (Mouse-ear cress)

       4       7887  Rattus norvegicus (Rat)

       5       6621  Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

       6       5984  Bos taurus (Bovine)

       7       5097  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)

       8       4431  Escherichia coli (strain K12)

       9       4185  Bacillus subtilis (strain 168)

      10       4127  Dictyostelium discoideum (Slime mold)

      11       3461  Caenorhabditis elegans

      12       3382  Xenopus laevis (African clawed frog)

      13       3220  Drosophila melanogaster (Fruit fly)

      14       3130  Oryza sativa subsp. japonica (Rice)

      15       2916  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2257  Gallus gallus (Chicken)

      17       2218  Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)

      18       2042  Mycobacterium tuberculosis

      19       2015  Escherichia coli O157:H7

      20       1787  Methanocaldococcus jannaschii  

      21       1772  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

      22       1707  Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

      23       1699  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

      24       1684  Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

      25       1679  Shigella flexneri

      26       1413  Sus scrofa (Pig)

      27       1346  Salmonella typhi

      28       1258  Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)

      29       1242  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

      30       1170  Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)

      31       1044  Synechocystis sp. (strain PCC 6803 / Kazusa)

      32       1019  Yersinia pestis

      33       1017  Archaeoglobus fulgidus 

      34        953  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

      35        930  Salmonella paratyphi A (strain ATCC 9150 / SARB42)

      36        926  Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)  

      37        925  Staphylococcus aureus (strain N315)

      38        924  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      39        909  Acanthamoeba polyphaga mimivirus (APMV)

      40        905  Kluyveromyces lactis   

      41        899  Staphylococcus aureus (strain COL)

      42        895  Staphylococcus aureus (strain MW2)

      43        889  Escherichia coli O6:K15:H31 (strain 536 / UPEC)

      44        889  Staphylococcus aureus (strain MSSA476)

      45        889  Oryctolagus cuniculus (Rabbit)

      46        888  Staphylococcus aureus (strain MRSA252)

      47        882  Salmonella choleraesuis (strain SC-B67)

      48        878  Shigella sonnei (strain Ss046)

      49        870  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      50        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      51        862  Candida glabrata   

      52        852  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      53        841  Escherichia coli O9:H4 (strain HS)

      54        837  Neurospora crassa 

      55        834  Escherichia coli O139:H28 (strain E24377A / ETEC)

      56        829  Shigella boydii serotype 4 (strain Sb227)

      57        825  Escherichia coli (strain UTI89 / UPEC)

      58        821  Shigella dysenteriae serotype 1 (strain Sd197)

      59        819  Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)

      60        807  Canis familiaris (Dog) (Canis lupus familiaris)

      61        791  Escherichia coli (strain SMS-3-5 / SECEC)

      62        788  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      63        783  Erwinia carotovora subsp. atroseptica (strain SCRI 1043 / ATCC BAA-672) 

      64        783  Aquifex aeolicus (strain VF5)

      65        781  Emericella nidulans  

      66        775  Pasteurella multocida (strain Pm70)

      67        771  Escherichia coli (strain K12 / DH10B)

      68        765  Escherichia coli O127:H6 (strain E2348/69 / EPEC)

      69        765  Escherichia coli (strain K12 / MC4100 / BW2952)

      70        765  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      71        764  Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)

      72        762  Escherichia coli (strain 55989 / EAEC)

      73        761  Escherichia coli O8 (strain IAI1)

      74        760  Shigella flexneri serotype 5b (strain 8401)

      75        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      76        758  Staphylococcus epidermidis (strain ATCC 12228)

      77        756  Escherichia coli (strain SE11)

      78        756  Escherichia coli O45:K1 (strain S88 / ExPEC)

      79        753  Escherichia coli O7:K1 (strain IAI39 / ExPEC)

      80        748  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      81        745  Photorhabdus luminescens subsp. laumondii (strain TT01)

      82        740  Staphylococcus aureus (strain NCTC 8325)

      83        736  Bacillus anthracis

      84        736  Bacillus halodurans 

      85        735  Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)

      86        735  Zea mays (Maize)

      87        733  Vibrio vulnificus (strain CMCP6)

      88        731  Escherichia coli O81 (strain ED1a)

      89        721  Salmonella enteritidis PT4 (strain P125109)

      90        717  Vibrio vulnificus (strain YJ016)

      91        716  Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)

      92        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      93        714  Salmonella paratyphi A (strain AKU_12601)

      94        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      95        713  Enterobacter sp. (strain 638)

      96        713  Salmonella agona (strain SL483)

      97        713  Escherichia coli O1:K1 / APEC

      98        713  Salmonella newport (strain SL254)

      99        713  Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)

     100        712  Salmonella schwarzengrund (strain CVM19633)

     101        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     102        710  Salmonella heidelberg (strain SL476)

     103        702  Salmonella dublin (strain CT_02021853)

     104        699  Pseudomonas putida (strain KT2440)

     105        698  Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)

     106        696  Klebsiella pneumoniae (strain 342)

     107        695  Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)

     108        691  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     109        689  Pan troglodytes (Chimpanzee)

     110        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     111        683  Salmonella gallinarum (strain 287/91 / NCTC 13346)

     112        678  Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

     113        675  Pseudomonas syringae pv. tomato (strain DC3000)

     114        670  Serratia proteamaculans (strain 568)

     115        668  Mycobacterium leprae (strain TN)

     116        667  Yersinia pestis (strain Pestoides F)

     117        667  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     118        666  Staphylococcus aureus (strain USA300)

     119        659  Bradyrhizobium diazoefficiens 

     120        658  Escherichia coli

     121        658  Rhizobium sp. (strain NGR234)

     122        654  Bacillus cereus (strain ATCC 14579 / DSM 31)

     123        653  Debaryomyces hansenii   

     124        646  Oryza sativa subsp. indica (Rice)

     125        644  Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)

     126        643  Staphylococcus aureus (strain bovine RF122 / ET3-1)

     127        642  Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)

     128        638  Yersinia pseudotuberculosis serotype O:3 (strain YPIII)

     129        635  Shewanella oneidensis (strain MR-1)

     130        634  Yersinia pseudotuberculosis serotype IB (strain PB1/+)

     131        634  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

     132        622  Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)

     133        616  Methanothermobacter thermautotrophicus  

     134        616  Treponema pallidum (strain Nichols)

     135        613  Staphylococcus haemolyticus (strain JCSC1435)

     136        607  Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)

     137        605  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

     138        604  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     139        602  Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)

     140        602  Photobacterium profundum (Photobacterium sp. (strain SS9))

     141        602  Staphylococcus saprophyticus subsp. saprophyticus 

     142        601  Salmonella paratyphi C (strain RKS4594)

     143        600  Yersinia pestis bv. Antiqua (strain Angola)

     144        591  Bacillus cereus (strain ATCC 10987)

     145        591  Listeria innocua serovar 6a (strain CLIP 11262)

     146        589  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     147        587  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     148        586  Rickettsia prowazekii (strain Madrid E)

     149        579  Neisseria meningitidis serogroup B (strain MC58)

     150        576  Brucella suis biovar 1 (strain 1330)

     151        573  Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

     152        572  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     153        568  Caenorhabditis briggsae

     154        567  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     155        566  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     156        566  Pseudomonas syringae pv. syringae (strain B728a)

     157        565  Caulobacter crescentus (strain ATCC 19089 / CB15)

     158        564  Bacillus licheniformis (strain DSM 13 / ATCC 14580)

     159        564  Vibrio fischeri (strain ATCC 700601 / ES114)

     160        564  Pseudomonas aeruginosa (strain UCBPP-PA14)

     161        562  Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)

     162        561  Bacillus cereus (strain ZK / E33L)

     163        557  Clostridium acetobutylicum 

     164        556  Xanthomonas axonopodis pv. citri (strain 306)

     165        552  Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831)

     166        552  Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)

     167        552  Pseudomonas fluorescens (strain Pf0-1)

     168        546  Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)

     169        545  Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6)

     170        534  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

     171        533  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

     172        531  Erwinia tasmaniensis (strain DSM 17950 / Et1/99)

     173        529  Sodalis glossinidius (strain morsitans)

     174        529  Listeria monocytogenes serotype 4b (strain F2365)

     175        525  Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) 

     176        522  Xylella fastidiosa (strain 9a5c)

     177        515  Chromobacterium violaceum 

     178        515  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     179        513  Corynebacterium glutamicum 

     180        513  Vibrio cholerae serotype O1 (strain ATCC 39541 / Ogawa 395 / O395)

     181        512  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     182        511  Pseudomonas aeruginosa (strain PA7)

     183        510  Haemophilus ducreyi (strain 35000HP / ATCC 700724)

     184        508  Staphylococcus aureus (strain Newman)

     185        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

     186        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     187        507  Geobacillus kaustophilus (strain HTA426)

     188        506  Streptomyces avermitilis 

     189        503  Deinococcus radiodurans 

     190        502  Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

     191        500  Pseudomonas entomophila (strain L48)

     192        499  Brucella abortus biovar 1 (strain 9-941)

     193        497  Rickettsia conorii (strain ATCC VR-613 / Malish 7)

     194        496  Bacillus clausii (strain KSM-K16)

     195        495  Burkholderia pseudomallei (strain K96243)

     196        495  Haemophilus influenzae (strain 86-028NP)

     197        494  Proteus mirabilis (strain HI4320)

     198        492  Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)

     199        492  Bacillus amyloliquefaciens (strain FZB42)

     200        491  Xanthomonas campestris pv. campestris (strain 8004)

     201        490  Vibrio campbellii (strain ATCC BAA-1116 / BB120)

     202        487  Shewanella sp. (strain MR-7)

     203        486  Mannheimia succiniciproducens (strain MBEL55E)

     204        484  Pseudomonas aeruginosa (strain LESB58)

     205        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     206        484  Shewanella sp. (strain MR-4)

     207        483  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     208        483  Methanosarcina mazei  

     209        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     210        482  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     211        482  Thermosynechococcus elongatus (strain BP-1)

     212        479  Pyrococcus horikoshii 

     213        479  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     214        477  Pseudomonas putida (strain F1 / ATCC 700007)

     215        476  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     216        475  Brucella abortus (strain 2308)

     217        475  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     218        474  Burkholderia sp. (strain 383) (Burkholderia cepacia 

     219        473  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     220        470  Pyrococcus abyssi (strain GE5 / Orsay)

     221        468  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     222        468  Clostridium perfringens (strain 13 / Type A)

     223        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     224        466  Shewanella frigidimarina (strain NCIMB 400)

     225        466  Pseudomonas putida (strain GB-1)

     226        466  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     227        464  Nicotiana tabacum (Common tobacco)

     228        464  Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240)

     229        463  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     230        463  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     231        463  Shewanella sp. (strain ANA-3)

     232        462  Burkholderia mallei (strain ATCC 23344)

     233        461  Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

     234        461  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     235        459  Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) (Ralstonia eutropha 

     236        458  Enterococcus faecalis (strain ATCC 700802 / V583)

     237        456  Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)

     238        455  Staphylococcus aureus (strain JH1)

     239        454  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     240        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     241        453  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     242        453  Pseudomonas putida (strain W619)

     243        453  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     244        452  Ovis aries (Sheep)

     245        452  Shewanella baltica (strain OS185)

     246        451  Aeromonas salmonicida (strain A449)

     247        450  Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)

     248        450  Dechloromonas aromatica (strain RCB)

     249        449  Thermoanaerobacter tengcongensis  

     250        449  Staphylococcus aureus (strain JH9)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19069 (  4%)

    Bacteria         329341 ( 61%)

    Eukaryota        177669 ( 33%)

    Viruses           16424 (  3%)





   Within Eukaryota:



   



    Category            sequences (% of Eukaryota) (% of the complete database)

     Human                  20271 ( 11%)           (  4%)

     Other Mammalia         46009 ( 26%)           (  8%)

     Other Vertebrata       17605 ( 10%)           (  3%)

     Viridiplantae          34824 ( 20%)           (  6%)

     Fungi                  31077 ( 17%)           (  6%)

     Insecta                 8728 (  5%)           (  2%)

     Nematoda                4337 (  2%)           (  1%)

     Other                  14818 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9084             1001-1100     3767

                 51- 100   41517             1101-1200     2615

                101- 150   57896             1201-1300     2033

                151- 200   57867             1301-1400     1907

                201- 250   56649             1401-1500     1525

                251- 300   50187             1501-1600      741

                301- 350   50356             1601-1700      573

                351- 400   43607             1701-1800      476

                401- 450   35692             1801-1900      432

                451- 500   28725             1901-2000      354

                501- 550   20460             2001-2100      216

                551- 600   14680             2101-2200      295

                601- 650   12320             2201-2300      299

                651- 700    8896             2301-2400      184

                701- 750    7328             2401-2500      139

                751- 800    5230             >2500         1101

                801- 850    4561

                851- 900    5049

                901- 950    3897

                951-1000    2768



   





   The average sequence length in UniProtKB/Swiss-Prot is 355 amino acids.



   The shortest sequence is   GWA_SEPOF (P83570):     2 amino acids.

   The longest sequence is  TITIN_MOUSE (A2ASS6): 35213 amino acids.





4.  JOURNAL CITATIONS



   Note: the following citation statistics reflect the number of distinct

         journal citations.



   Total number of journals cited in this release of UniProtKB/Swiss-Prot: 2382





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  770

                       2x:  317

                       3x:  161

                       4x:  118

                       5x:   86

                       6x:   79

                       7x:   56

                       8x:   46

                       9x:   34

                      10x:   37

                  11- 20x:  185

                  21- 50x:  194

                  51-100x:  108

                    >100x:  191





   4.2  List of the most cited journals in UniProtKB/Swiss-Prot



   Nb    Citations   Journal name

   --    ---------   -------------------------------------------------------------

    1        21760   Journal of Biological Chemistry

    2         9851   Proceedings of the National Academy of Sciences of the U.S.A.

    3         5856   Journal of Bacteriology

    4         5131   Biochemical and Biophysical Research Communications

    5         4633   Nucleic Acids Research

    6         4629   Gene

    7         4598   Biochemistry

    8         4436   FEBS Letters

    9         4318   The EMBO Journal

   10         3994   Molecular and Cellular Biology

   11         3852   Nature

   12         3713   Journal of Molecular Biology

   13         3283   Biochimica et Biophysica Acta

   14         3262   European Journal of Biochemistry

   15         3140   Cell

   16         2662   Journal of Virology

   17         2565   Biochemical Journal

   18         2553   Science

   19         2514   Genomics

   20         2144   Molecular Microbiology

   21         1952   Plant Physiology

   22         1941   Journal of Cell Biology

   23         1692   The American Journal of Human Genetics

   24         1676   Plant Molecular Biology

   25         1641   Genes and Development

   26         1552   Virology

   27         1547   Nature Genetics

   28         1507   Human Molecular Genetics

   29         1457   Oncogene

   30         1409   Molecular Biology of the Cell

   31         1402   The Plant Cell

   32         1390   Development

   33         1353   Molecular and General Genetics

   34         1334   Human Mutation

   35         1265   The Plant Journal

   36         1259   Journal of Biochemistry

   37         1235   Molecular Cell

   38         1201   Journal of Immunology

   39         1130   Genetics

   40         1124   Structure

   41         1042   Journal of General Virology

   42         1006   Blood

   43          993   Journal of Cell Science

   44          978   Infection and Immunity

   45          952   Archives of Biochemistry and Biophysics

   46          908   Microbiology

   47          857   Developmental Biology

   48          847   Current Biology

   49          823   Cancer Research

   50          797   Yeast

   51          775   PLoS ONE

   52          749   FEMS Microbiology Letters

   53          711   Acta Crystallographica, Section D

   54          681   Journal of Neuroscience

   55          680   Protein Science

   56          676   Applied and Environmental Microbiology

   57          670   Toxicon

   58          636   Human Genetics

   59          630   Nature Structural Biology

   60          626   Mechanisms of Development

   61          610   Neuron

   62          587   Journal of Clinical Investigation

   63          569   American Journal of Physiology

   64          544   The Journal of Experimental Medicine

   65          543   Current Genetics

   66          519   Proteins

   67          507   Plant and Cell Physiology

   68          501   Molecular Endocrinology

   69          480   Mammalian Genome

   70          476   Journal of Neurochemistry

   71          467   Nature Cell Biology

   72          460   Immunogenetics

   73          459   Bioscience, Biotechnology, and Biochemistry

   74          454   Endocrinology

   75          448   The Journal of Clinical Endocrinology and Metabolism

   76          448   Journal of Medical Genetics

   77          435   Molecular and Biochemical Parasitology

   78          402   Journal of Molecular Evolution

   79          389   Experimental Cell Research

   80          380   Molecular Biology and Evolution

   81          377   DNA and Cell Biology

   82          367   DNA Sequence

   83          364   Peptides

   84          364   Nature Structural and Molecular Biology

   85          350   The FEBS Journal

   86          345   RNA

   87          341   Developmental Cell

   88          333   Antimicrobial Agents and Chemotherapy

   89          330   Brain Research. Molecular Brain Research

   90          326   Tissue Antigens

   91          324   Eukaryotic Cell

   92          321   Comparative Biochemistry and Physiology

   93          316   Journal of Investigative Dermatology

   94          316   Planta

   95          313   Molecular Pharmacology

   96          296   Biology of Reproduction

   97          294   Biological Chemistry Hoppe-Seyler

   98          289   Neurology

   99          280   Cytogenetics and Cell Genetics

  100          279   Developmental Dynamics

  101          273   EMBO Reports

  102          270   Virus Research

  103          269   Biochimie

  104          267   Genome Research

  105          267   Immunity

  106          264   Genes to Cells

  107          262   The FASEB Journal

  108          259   Journal of General Microbiology

  109          252   The New England Journal of Medicine

  110          248   Molecular Plant-Microbe Interactions

  111          238   Journal of the American Chemical Society

  112          235   European Journal of Immunology

  113          233   Annals of Neurology

  114          233   European Journal of Human Genetics

  115          227   Acta Crystallographica, Section F

  116          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  117          216   DNA Research

  118          214   PLoS Genetics

  119          214   Journal of Human Genetics

  120          211   Investigative Ophthalmology and Visual Science

  121          208   Archives of Microbiology

  122          205   Journal of Experimental Botany

  123          205   Nature Immunology

  124          204   BMC Genomics

  125          202   Journal of Cellular Biochemistry

  126          195   American Journal of Medical Genetics. Part A

  127          194   Journal of Medicinal Chemistry

  128          192   Molecular and Cellular Endocrinology

  129          191   Glycobiology

  130          191   Archives of Virology

  131          188   Clinical Genetics

  132          187   Molecular Immunology

  133          182   Circulation Research

  134          178   Diabetes

  135          175   Insect Biochemistry and Molecular Biology

  136          175   Traffic

  137          171   Cell Cycle

  138          170   Molecular Genetics and Metabolism

  139          169   Phytochemistry

  140          169   Molecular Phylogenetics and Evolution

  141          168   American Journal of Medical Genetics

  142          166   International Journal of Cancer

  143          163   PLoS Pathogens

  144          162   Protein Expression and Purification

  145          160   Molecular Reproduction and Development

  146          159   DNA

  147          158   Applied Microbiology and Biotechnology

  148          157   Molecular and Cellular Neuroscience

  149          157   Biological Chemistry

  150          156   Molecular Genetics and Genomics





5.  STATISTICS FOR SOME LINE TYPES



The following table summarizes the total number of some UniProtKB/Swiss-Prot lines,

as well as the number of entries with at least one such line, and the

frequency of the lines.



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry

------------------------------------  -------- ---------  ---------



References (RL)                      1066266                 1.97                                         

   Journal                            861576     423635      1.59       1                                 

   Submitted to EMBL/GenBank/DDBJ     195495     174426      0.36       2                                 

   Submitted to other databases         6943       6462      0.01       3                                 

   Book citation                         725        711     <0.01       4                                 

   Plant Gene Register                   591        579     <0.01       5                                 

   Thesis                                418        415     <0.01       6                                 

   Unpublished observations              322        318     <0.01       7                                 

   Patent                                190        187     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 346669



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

------------------------------------  -------- ---------  ---------  ----

Comments (CC)                        2471053                 4.55                                         

   ALLERGEN                              661        661     <0.01      25                                 

   ALTERNATIVE PRODUCTS                22562      22562      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        5457       5457      0.01      23                                 

   BIOTECHNOLOGY                         369        367     <0.01      28                                 

   CATALYTIC ACTIVITY                 246895     222801      0.46       5                                 

   CAUTION                              9743       9562      0.02      18                                 

   COFACTOR                           112404     102917      0.21       7                                 

   DEVELOPMENTAL STAGE                 10194      10194      0.02      17                                 

   DISEASE                              5521       3707      0.01      22                                 

   DISRUPTION PHENOTYPE                 6699       6699      0.01      20                                 

   DOMAIN                              41348      36031      0.08      10                                 

   ENZYME REGULATION                   12172      12172      0.02      16                                 

   FUNCTION                           428885     411252      0.79       2                                 

   INDUCTION                           15886      15886      0.03      14                                 

   INTERACTION                         12500      12500      0.02      15                                 

   MASS SPECTROMETRY                    5699       4341      0.01      21                                 

   MISCELLANEOUS                       33279      30728      0.06      12                                 

   PATHWAY                            132485     120590      0.24       6                                 

   PHARMACEUTICAL                         94         94     <0.01      29                                 

   POLYMORPHISM                         1033        979     <0.01      24                                 

   PTM                                 45951      35704      0.08       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    41553      41553      0.08       9                                 

   SIMILARITY                         647035     517978      1.19       1                                 

   SUBCELLULAR LOCATION               330313     324155      0.61       3                                 

   SUBUNIT                            251766     251766      0.46       4                                 

   TISSUE SPECIFICITY                  39860      39860      0.07      11                                 

   TOXIC DOSE                            571        534     <0.01      27                                 

   WEB RESOURCE                         9491       7544      0.02      19                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

------------------------------------  -------- ---------  ---------  ----

Features (FT)                        3825960                 7.05                                         

   ACT_SITE                           146775      89807      0.27       9                                 

   BINDING                            311477      83207      0.57       4                                 

   CA_BIND                              3936       1647      0.01      35                                 

   CARBOHYD                           108537      27751      0.20      15                                 

   CHAIN                              549610     536221      1.01       1                                 

   COILED                              20554      14118      0.04      26                                 

   COMPBIAS                            55312      29420      0.10      18                                 

   CONFLICT                           129273      45286      0.24      12                                 

   CROSSLNK                             7019       4019      0.01      34                                 

   DISULFID                           112304      30718      0.21      14                                 

   DNA_BIND                            10525       9584      0.02      31                                 

   DOMAIN                             164606      97970      0.30       7                                 

   HELIX                              191420      18451      0.35       6                                 

   INIT_MET                            16898      16898      0.03      27                                 

   INTRAMEM                             2193        951     <0.01      37                                 

   LIPID                               12140       7731      0.02      30                                 

   METAL                              333332      82398      0.61       3                                 

   MOD_RES                            161817      60948      0.30       8                                 

   MOTIF                               37101      24076      0.07      24                                 

   MUTAGEN                             47100      10843      0.09      20                                 

   NON_CONS                             2048        750     <0.01      38                                 

   NON_STD                               356        281     <0.01      39                                 

   NON_TER                             12221       9341      0.02      29                                 

   NP_BIND                            125132      75468      0.23      13                                 

   PEPTIDE                             10391       7096      0.02      32                                 

   PROPEP                              12834      11050      0.02      28                                 

   REGION                             144930      73130      0.27      10                                 

   REPEAT                              96731      14266      0.18      16                                 

   SIGNAL                              38678      38668      0.07      23                                 

   SITE                                48077      26642      0.09      19                                 

   STRAND                             200766      17424      0.37       5                                 

   TOPO_DOM                           132005      27320      0.24      11                                 

   TRANSIT                              8559       8453      0.02      33                                 

   TRANSMEM                           357761      73960      0.66       2                                 

   TURN                                46671      14975      0.09      22                                 

   UNSURE                               3404        726      0.01      36                                 

   VAR_SEQ                             46846      19632      0.09      21                                 

   VARIANT                             87119      16854      0.16      17                                 

   ZN_FING                             29502      12982      0.05      25                                 



Total number of feature keys: 39







                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank      Category

------------------------------------  -------- ---------  ---------  ----      -------------------------------------------

Cross-references (DR)               16451949                30.33                                                           

   Allergome                            1621       1057     <0.01     103      Protein family/group databases               

   ArachnoServer                         763        755     <0.01     115      Organism-specific databases                  

   ArrayExpress                        33242      33242      0.06      50      Gene expression databases                    

   Bgee                                38824      38824      0.07      46      Gene expression databases                    

   BindingDB                            5033       5033      0.01      88      Chemistry                                    

   BioCyc                             323145     307249      0.60      20      Enzyme and pathway databases                 

   BioGrid                             38813      38470      0.07      47      Protein-protein interaction databases        

   BRENDA                               4346       4335      0.01      93      Enzyme and pathway databases                 

   CAZy                                 7683       6916      0.01      76      Protein family/group databases               

   CGD                                   831        809     <0.01     111      Organism-specific databases                  

   ChEMBL                               5709       5709      0.01      81      Chemistry                                    

   ChiTaRS                             12550      12545      0.02      71      Other                                        

   CleanEx                             30070      29430      0.06      52      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     127      2D gel databases                             

   ConoServer                            926        844     <0.01     108      Organism-specific databases                  

   CTD                                 71009      70288      0.13      38      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      82      Organism-specific databases                  

   dictyBase                            4203       4087      0.01      95      Organism-specific databases                  

   DIP                                 15049      14974      0.03      68      Protein-protein interaction databases        

   DisProt                               608        605     <0.01     118      3D structure databases                       

   DMDM                                16750      16747      0.03      64      Polymorphism databases                       

   DNASU                               18744      18673      0.03      60      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     149        147     <0.01     126      2D gel databases                             

   DrugBank                             5319       1628      0.01      85      Chemistry                                    

   EchoBASE                             4161       4161      0.01      96      Organism-specific databases                  

   EcoGene                              4292       4290      0.01      94      Organism-specific databases                  

   eggNOG                             431612     431612      0.80      10      Phylogenomic databases                       

   EMBL                               947989     531183      1.75       3      Sequence databases                           

   Ensembl                             85104      49022      0.16      35      Genome annotation databases                  

   EnsemblBacteria                    348442     328000      0.64      18      Genome annotation databases                  

   EnsemblFungi                        18549      18249      0.03      61      Genome annotation databases                  

   EnsemblMetazoa                      12468       9349      0.02      73      Genome annotation databases                  

   EnsemblPlants                       16620      14844      0.03      66      Genome annotation databases                  

   EnsemblProtists                      4576       4449      0.01      92      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     128      Organism-specific databases                  

   EuPathDB                              776        776     <0.01     112      Organism-specific databases                  

   EvolutionaryTrace                   16661      16661      0.03      65      Other                                        

   FlyBase                              5922       5548      0.01      80      Organism-specific databases                  

   Gene3D                             357757     272906      0.66      17      Family and domain databases                  

   GeneCards                           20899      19800      0.04      57      Organism-specific databases                  

   GeneFarm                             3229       3218      0.01      97      Organism-specific databases                  

   GeneID                             498045     465537      0.92       6      Genome annotation databases                  

   GeneTree                            38132      38114      0.07      48      Phylogenomic databases                       

   Genevestigator                      67854      67854      0.13      40      Gene expression databases                    

   GeneWiki                            10373      10286      0.02      74      Other                                        

   GenoList                             7071       7059      0.01      77      Organism-specific databases                  

   GenomeRNAi                          21332      21332      0.04      56      Other                                        

   GO                                2516577     513134      4.64       1      Ontologies                                   

   Gramene                              6092       6092      0.01      79      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  1797       1797     <0.01     102      Chemistry                                    

   H-InvDB                              5590       4770      0.01      83      Organism-specific databases                  

   HAMAP                              322508     319613      0.59      21      Family and domain databases                  

   HGNC                                19908      19742      0.04      59      Organism-specific databases                  

   HOGENOM                            386334     386334      0.71      14      Phylogenomic databases                       

   HOVERGEN                            75642      75642      0.14      36      Phylogenomic databases                       

   HPA                                 22364      15992      0.04      55      Organism-specific databases                  

   InParanoid                          70557      70557      0.13      39      Phylogenomic databases                       

   IntAct                              41210      41210      0.08      45      Protein-protein interaction databases        

   InterPro                          1832291     520517      3.38       2      Family and domain databases                  

   KEGG                               471277     441759      0.87       7      Genome annotation databases                  

   KO                                 370718     370251      0.68      16      Phylogenomic databases                       

   LegioList                             765        763     <0.01     114      Organism-specific databases                  

   Leproma                               671        668     <0.01     117      Organism-specific databases                  

   MaizeGDB                              502        497     <0.01     121      Organism-specific databases                  

   MEROPS                              12535      12535      0.02      72      Protein family/group databases               

   MGI                                 16569      16525      0.03      67      Organism-specific databases                  

   MIM                                 18498      13879      0.03      62      Organism-specific databases                  

   MINT                                31572      31572      0.06      51      Protein-protein interaction databases        

   mycoCLAP                              285        279     <0.01     124      Protein family/group databases               

   NextBio                             71121      71121      0.13      37      Other                                        

   neXtProt                            20116      20116      0.04      58      Organism-specific databases                  

   OGP                                   377        377     <0.01     123      2D gel databases                             

   OMA                                401030     401030      0.74      11      Phylogenomic databases                       

   Orphanet                             5588       2980      0.01      84      Organism-specific databases                  

   OrthoDB                            390523     390523      0.72      13      Phylogenomic databases                       

   PANTHER                            191653     180129      0.35      25      Family and domain databases                  

   PATRIC                             309171     309139      0.57      22      Genome annotation databases                  

   PaxDb                               66737      66737      0.12      41      Proteomic databases                          

   PDB                                104115      20446      0.19      32      3D structure databases                       

   PDBsum                             104115      20446      0.19      31      3D structure databases                       

   PeptideAtlas                         5162       5162      0.01      87      Proteomic databases                          

   PeroxiBase                            772        756     <0.01     113      Protein family/group databases               

   Pfam                               726000     499974      1.34       4      Family and domain databases                  

   PharmGKB                            18386      18358      0.03      63      Organism-specific databases                  

   PhosphoSite                         33568      33568      0.06      49      PTM databases                                

   PhosSite                              699        687     <0.01     116      PTM databases                                

   PhylomeDB                           27778      27778      0.05      54      Phylogenomic databases                       

   PIR                                119258     109079      0.22      30      Sequence databases                           

   PIRSF                              101680     100720      0.19      33      Family and domain databases                  

   PMAP-CutDB                           1462       1462     <0.01     104      Other                                        

   PomBase                              5015       4968      0.01      89      Organism-specific databases                  

   PptaseDB                               40         40     <0.01     129      Protein family/group databases               

   PRIDE                              123429     123429      0.23      29      Proteomic databases                          

   PRINTS                             136731     120464      0.25      27      Family and domain databases                  

   PRO                                 57896      57896      0.11      42      Other                                        

   ProDom                              29305      29126      0.05      53      Family and domain databases                  

   ProMEX                                868        868     <0.01     110      Proteomic databases                          

   PROSITE                            432846     282055      0.80       9      Family and domain databases                  

   ProtClustDB                        344792     344792      0.64      19      Phylogenomic databases                       

   ProteinModelPortal                 436590     436590      0.80       8      3D structure databases                       

   PseudoCAP                            1266       1257     <0.01     105      Organism-specific databases                  

   Reactome                            14504       8313      0.03      69      Enzyme and pathway databases                 

   REBASE                                403        403     <0.01     122      Protein family/group databases               

   RefSeq                             548040     474621      1.01       5      Sequence databases                           

   REPRODUCTION-2DPAGE                  1258       1037     <0.01     106      2D gel databases                             

   RGD                                  7807       7803      0.01      75      Organism-specific databases                  

   SABIO-RK                             2823       2823      0.01      99      Enzyme and pathway databases                 

   SGD                                  6640       6635      0.01      78      Organism-specific databases                  

   SignaLink                            2959       2959      0.01      98      Enzyme and pathway databases                 

   SMART                              168465     126201      0.31      26      Family and domain databases                  

   SMR                                220871     220871      0.41      24      3D structure databases                       

   STRING                             397247     397246      0.73      12      Protein-protein interaction databases        

   SUPFAM                             378170     292646      0.70      15      Family and domain databases                  

   SWISS-2DPAGE                         1182       1181     <0.01     107      2D gel databases                             

   TAIR                                12674      12618      0.02      70      Organism-specific databases                  

   TCDB                                 5167       5139      0.01      86      Protein family/group databases               

   TIGRFAMs                           290141     270091      0.53      23      Family and domain databases                  

   TreeFam                             44648      44643      0.08      43      Phylogenomic databases                       

   TubercuList                          2055       2019     <0.01     101      Organism-specific databases                  

   UCD-2DPAGE                            509        500     <0.01     120      2D gel databases                             

   UCSC                                44349      44349      0.08      44      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     125      PTM databases                                

   UniGene                            100056      90786      0.18      34      Sequence databases                           

   UniPathway                         132312     120425      0.24      28      Enzyme and pathway databases                 

   VectorBase                            606        588     <0.01     119      Genome annotation databases                  

   World-2DPAGE                          921        910     <0.01     109      2D gel databases                             

   WormBase                             5006       3991      0.01      90      Organism-specific databases                  

   Xenbase                              4757       4751      0.01      91      Organism-specific databases                  

   ZFIN                                 2755       2755      0.01     100      Organism-specific databases                  



Total number of cross-referenced databases: 129



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



   Ala (A) 8.25   Gln (Q) 3.93   Leu (L) 9.66   Ser (S) 6.57

   Arg (R) 5.53   Glu (E) 6.75   Lys (K) 5.84   Thr (T) 5.34

   Asn (N) 4.06   Gly (G) 7.07   Met (M) 2.41   Trp (W) 1.08

   Asp (D) 5.45   His (H) 2.27   Phe (F) 3.86   Tyr (Y) 2.92

   Cys (C) 1.37   Ile (I) 5.95   Pro (P) 4.70   Val (V) 6.86



   Asx (B) 0.000  Glx (Z) 0.000  Xaa (X) 0.00



   



   Legend: gray = aliphatic, red = acidic, green = small hydroxy,

           blue = basic, black = aromatic, white = amide, yellow = sulfur





   6.2  Classification of the amino acids by their frequency



   Leu, Ala, Gly, Val, Glu, Ser, Ile, Lys, Arg, Asp, Thr, Pro, Asn, Gln,

   Phe, Tyr, Met, His, Cys, Trp





7.  MISCELLANEOUS STATISTICS



4465 entries are encoded on a mitochondrion, and 3734 are encoded on a plasmid.



12188 entries are encoded on a plastid, 

of which 21 are encoded on apicoplasts, 

11623 on chloroplasts, 

51 on organellar chromatophores,

145 on cyanelles, 

149 on non-photosynthetic plastids and 

199 on unspecified types of plastid.



Number of entries with at least one sequence correction: 75474